diff --git a/README.md b/README.md index 5b106e1f781e1988516ad1adad9ca4a199793ee0..850f04b4ea311ea8b0604bf833ae2ff87df96c0a 100644 --- a/README.md +++ b/README.md @@ -11,9 +11,10 @@ Original code: <https://github.com/Hyojung-Choo/Myosoft/tree/Myosoft-hub> ## [`1_identify_fibers.py`](1_identify_fibers.py) -- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose) segmentation, filter them according to the morphometric gates and save the - corresponding ROIs. - - Need to be installed ont the machine where the script is run. Follow [this guide](https://wiki.biozentrum.unibas.ch/display/IMCF/Cellpose+python+environment) to create the environment. +- Will identify all fibers based on the membrane staining using [Cellpose](https://github.com/MouseLand/cellpose) + segmentation, filter them according to the morphometric gates and save the corresponding ROIs. + - Need to be installed on the machine where the script is run. Follow + [this guide](https://wiki.biozentrum.unibas.ch/display/IMCF/Cellpose+python+environment) to create the environment. Please don't recreate the environment if it already exists! - Will now also save the Cellpose segmentation as a binary so it can be edited manually. If you do so, you need to run the "extended particle analyzer" manually as well to choose & apply the morphometric gates.